Table 3

Top SNP associations with lichen planus

Discovery setValidation set
SNPPosition (bp,hg19)FunctionGeneAmino acid changeVariationCase MAF (N=97)Control MAF (N=7321)Fisher's p valueOR (95% CI)FDRCase MAF (N=81)Control MAF (N=3806)Fisher's p valueOR (95% CI)Meta- analysis p value
rs693077732 351 566IntergenicC6orf10, HCG23C/T0.230.126.8E-062.3 (1.6 to 3.2)0.28
rs424816632 366 421IntronicBTNL2T/C0.300.181.4E-052.0 (1.5 to 2.8)0.380.250.170.0131.6 (1.1 to 2.3)8.3E-07
rs104905632 634 369ExonicHLA-DQB1A6SC/A0.320.161.8E-072.4 (1.8 to 3.2)0.03
rs1319247132 671 103IntergenicHLA-DQB1, HLA-DQA2T/C0.290.148.4E-082.5 (1.8 to 3.4)0.020.230.140.00381.8 (1.2 to 2.6)1.9E-09
rs179427532 671 248IntergenicHLA-DQB1, HLA-DQA2G/A0.340.171.8E-082.5 (1.8 to 3.4)0.0070.230.170.0311.5 (1.0 to 2.2)3.3E-09
rs285710632 787 570IntergenicHLA-DOB, TAP2T/C0.330.201.4E-052 (1.5 to 2.7)0.380.280.190.00511.7 (1.2 to 2.4)3.4E-07
  • FDR, false discovery rate; MAF, minor allele frequency; N, number of cases or controls.